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Issue in running test file #29

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Issue in running test file#29

Description

@SelfShubham
SelfShubham
opened on Jul 7, 2025

Thank you for making this very comprehensive tool for phages.
What can be the possible reason for the error I am facing.

nextflow run deng-lab/viroprofiler -r main -profile docker,test

N E X T F L O W ~ version 25.04.6

Launching https://github.com/deng-lab/viroprofiler [kickass_thompson] DSL2 - revision: c2a1f18 [main]

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ViroProfiler v0.2.4

Core Nextflow options
revision : main
runName : kickass_thompson
containerEngine : docker
container : [withLabel:viroprofiler_base:denglab/viroprofiler-base:v0.2, withLabel:viroprofiler_abundance:denglab/viroprofiler-abundance:v0.2, withLabel:viroprofiler_bracken:denglab/viroprofiler-bracken:v0.2, withLabel:viroprofiler_vibrant:denglab/viroprofiler-vibrant:v0.2, withLabel:viroprofiler_binning:denglab/viroprofiler-binning:v0.2, withLabel:viroprofiler_geneannot:denglab/viroprofiler-geneannot:v0.2, withLabel:viroprofiler_host:denglab/viroprofiler-host:v0.1, withLabel:viroprofiler_replicyc:denglab/viroprofiler-replicyc:v0.1, withLabel:viroprofiler_taxa:denglab/viroprofiler-taxa:v0.1, withLabel:viroprofiler_virsorter2:denglab/viroprofiler-virsorter2:v0.2.5, withLabel:viroprofiler_vpfkit:denglab/viroprofiler-viewer]
launchDir : /home/ncim
workDir : /home/ncim/work
projectDir : /home/ncim/.nextflow/assets/deng-lab/viroprofiler
userName : ncim
profile : docker,test
configFiles : /home/ncim/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options
mode : all
input : https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv
db : /home/ncim/viroprofiler
outdir : output

QC
contamref_idx : /home/ncim/viroprofiler/contamination_refs/hg19/ref

Contig library parameters
assemblies : scaffolds

Others
use_iphop : true
use_dram : true

Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function

Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 24.h

!! Only displaying parameters that differ from the pipeline defaults !!

If you use ViroProfiler for your analysis please cite:

executor > local (17)
[6a/9edb79] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[9f/6112ec] process > VIROPROFILER:FASTP (HT04) [100%] 5 of 5 ✔
[17/d32dfe] process > VIROPROFILER:SPADES (UC20) [100%] 5 of 5 ✔
[48/81fa2d] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔
[40/749b8d] process > VIROPROFILER:CHECKV [ 0%] 0 of 1
[- ] process > VIROPROFILER:CONTIGLIB_CLUSTER -
[- ] process > VIROPROFILER:GENEPRED4CTG -
[- ] process > VIROPROFILER:NRPROT -
[- ] process > VIROPROFILER:NRGENE -
[- ] process > VIROPROFILER:CONTIGINDEX -
[- ] process > VIROPROFILER:MAPPING2CONTIGS2 -
[- ] process > VIROPROFILER:ABUNDANCE -
[- ] process > VIROPROFILER:VIBRANT -
[- ] process > VIROPROFILER:DVF -
[- ] process > VIROPROFILER:VIRCONTIGS_PRE -
[- ] process > VIROPROFILER:VIRSORTER2 -
[- ] process > VIROPROFILER:DRAMV -
[- ] process > VIROPROFILER:TAXONOMY_VCONTACT -
[- ] process > VIROPROFILER:TAXONOMY_MMSEQS -
[- ] process > VIROPROFILER:TAXONOMY_MERGE -
[- ] process > VIROPROFILER:VIRALHOST_IPHOP -
[- ] process > VIROPROFILER:BACPHLIP -
[- ] process > VIROPROFILER:RESULTS_TSE -
[- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > VIROPROFILER:MULTIQC -

ERROR ~ Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
Process VIROPROFILER:CHECKV terminated with an error exit status (1)

Command executed:

run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /home/ncim/viroprofiler/checkv
mv viruses.fna checkv_qc.fasta
while [ -s proviruses_nextInput.fna ] ; do
dir_new=run_$(date +"%Y%m%d%h%s")
run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /home/ncim/viroprofiler/checkv
cat $dir_new/viruses.fna >> checkv_qc.fasta
csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
cp quality_summary.tsv quality_summary_viruses.tsv
sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
cat $dir_new/proviruses_short.fna >> proviruses_short.fna
cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
cp $dir_new/proviruses_nextInput.fna .
sleep 1
done
seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

cat <<-END_VERSIONS > versions.yml
"VIROPROFILER:CHECKV":
CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:

CheckV v1.0.1: contamination
[1/8] Reading database info...
[2/8] Reading genome info...
[3/8] Calling genes with Prodigal...
[4/8] Reading gene info...
executor > local (17)
[6a/9edb79] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[9f/6112ec] process > VIROPROFILER:FASTP (HT04) [100%] 5 of 5 ✔
[17/d32dfe] process > VIROPROFILER:SPADES (UC20) [100%] 5 of 5 ✔
[48/81fa2d] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔
[40/749b8d] process > VIROPROFILER:CHECKV [ 0%] 0 of 1 ✘
[- ] process > VIROPROFILER:CONTIGLIB_CLUSTER -
[- ] process > VIROPROFILER:GENEPRED4CTG -
[- ] process > VIROPROFILER:NRPROT -
[- ] process > VIROPROFILER:NRGENE -
[- ] process > VIROPROFILER:CONTIGINDEX -
[- ] process > VIROPROFILER:MAPPING2CONTIGS2 -
[- ] process > VIROPROFILER:ABUNDANCE -
[- ] process > VIROPROFILER:VIBRANT -
[- ] process > VIROPROFILER:DVF -
[- ] process > VIROPROFILER:VIRCONTIGS_PRE -
[- ] process > VIROPROFILER:VIRSORTER2 -
[- ] process > VIROPROFILER:DRAMV -
[- ] process > VIROPROFILER:TAXONOMY_VCONTACT -
[- ] process > VIROPROFILER:TAXONOMY_MMSEQS -
[- ] process > VIROPROFILER:TAXONOMY_MERGE -
[- ] process > VIROPROFILER:VIRALHOST_IPHOP -
[- ] process > VIROPROFILER:BACPHLIP -
[- ] process > VIROPROFILER:RESULTS_TSE -
[- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > VIROPROFILER:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
**ERROR ~ Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
Process VIROPROFILER:CHECKV terminated with an error exit status (1)**

Command executed:

run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /home/ncim/viroprofiler/checkv
mv viruses.fna checkv_qc.fasta
while [ -s proviruses_nextInput.fna ] ; do
dir_new=run_$(date +"%Y%m%d%h%s")
run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /home/ncim/viroprofiler/checkv
cat $dir_new/viruses.fna >> checkv_qc.fasta
csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
cp quality_summary.tsv quality_summary_viruses.tsv
sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
cat $dir_new/proviruses_short.fna >> proviruses_short.fna
cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
cp $dir_new/proviruses_nextInput.fna .
sleep 1
done
seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

cat <<-END_VERSIONS > versions.yml
"VIROPROFILER:CHECKV":
CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:

CheckV v1.0.1: contamination
[1/8] Reading database info...
[2/8] Reading genome info...
[3/8] Calling genes with Prodigal...
[4/8] Reading gene info...
executor > local (17)
[6a/9edb79] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[9f/6112ec] process > VIROPROFILER:FASTP (HT04) [100%] 5 of 5 ✔
[17/d32dfe] process > VIROPROFILER:SPADES (UC20) [100%] 5 of 5 ✔
[48/81fa2d] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔
[40/749b8d] process > VIROPROFILER:CHECKV [ 0%] 0 of 1 ✘
[- ] process > VIROPROFILER:CONTIGLIB_CLUSTER -
[- ] process > VIROPROFILER:GENEPRED4CTG -
[- ] process > VIROPROFILER:NRPROT -
[- ] process > VIROPROFILER:NRGENE -
[- ] process > VIROPROFILER:CONTIGINDEX -
[- ] process > VIROPROFILER:MAPPING2CONTIGS2 -
[- ] process > VIROPROFILER:ABUNDANCE -
[- ] process > VIROPROFILER:VIBRANT -
[- ] process > VIROPROFILER:DVF -
[- ] process > VIROPROFILER:VIRCONTIGS_PRE -
[- ] process > VIROPROFILER:VIRSORTER2 -
[- ] process > VIROPROFILER:DRAMV -
[- ] process > VIROPROFILER:TAXONOMY_VCONTACT -
[- ] process > VIROPROFILER:TAXONOMY_MMSEQS -
[- ] process > VIROPROFILER:TAXONOMY_MERGE -
[- ] process > VIROPROFILER:VIRALHOST_IPHOP -
[- ] process > VIROPROFILER:BACPHLIP -
[- ] process > VIROPROFILER:RESULTS_TSE -
[- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > VIROPROFILER:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
**ERROR ~ Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
Process VIROPROFILER:CHECKV terminated with an error exit status (1)**

Command executed:

run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /home/ncim/viroprofiler/checkv
mv viruses.fna checkv_qc.fasta
while [ -s proviruses_nextInput.fna ] ; do
dir_new=run_$(date +"%Y%m%d%h%s")
run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /home/ncim/viroprofiler/checkv
cat $dir_new/viruses.fna >> checkv_qc.fasta
csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
cp quality_summary.tsv quality_summary_viruses.tsv
sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
cat $dir_new/proviruses_short.fna >> proviruses_short.fna
cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
cp $dir_new/proviruses_nextInput.fna .
sleep 1
done
seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

cat <<-END_VERSIONS > versions.yml
"VIROPROFILER:CHECKV":
CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:

CheckV v1.0.1: contamination
[1/8] Reading database info...
[2/8] Reading genome info...
[3/8] Calling genes with Prodigal...
[4/8] Reading gene info...
[5/8] Running hmmsearch...
[6/8] Annotating genes...
[7/8] Identifying host regions...
[8/8] Writing results...
Run time: 112.89 seconds
Peak mem: 0.25 GB

CheckV v1.0.1: completeness
[1/8] Skipping gene calling...
[2/8] Initializing queries and database...
[3/8] Running DIAMOND blastp search...
[4/8] Computing AAI...
[5/8] Running AAI based completeness estimation...
[6/8] Running HMM based completeness estimation...
[7/8] Determining genome copy number...
[8/8] Writing results...
Run time: 38.42 seconds
Peak mem: 1.96 GB

CheckV v1.0.1: complete_genomes
[1/7] Reading input sequences...
[2/7] Finding complete proviruses...
[3/7] Finding direct/inverted terminal repeats...
[4/7] Filtering terminal repeats...
[5/7] Checking genome for completeness...
[6/7] Checking genome for large duplications...
[7/7] Writing results...
Run time: 0.03 seconds
Peak mem: 1.96 GB

CheckV v1.0.1: quality_summary
[1/6] Reading input sequences...
[2/6] Reading results from contamination module...
[3/6] Reading results from completeness module...
[4/6] Reading results from complete genomes module...
[5/6] Classifying contigs into quality tiers...
[6/6] Writing results...
Run time: 0.01 seconds
Peak mem: 1.96 GB
Traceback (most recent call last):
File "/home/ncim/.nextflow/assets/deng-lab/viroprofiler/bin/correct_spades_contig_length.py", line 5, in
from Bio import SeqIO
ModuleNotFoundError: No module named 'Bio'

Work dir:
/home/ncim/work/40/749b8d4b26bd237c309b6d026db24e

Container:
denglab/viroprofiler-base:v0.2

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

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